This application is intended as an improvement over the alignment systems of the above-referenced Markle patent application. As described in the earlier Markle disclosure, periodic patterns on a mask and wafer can be used to perform automatic fine alignment in a scanning projection mask aligner during the scanning operation. However, in certain installations, particularly where the illumination of the target imprinted on the wafer is non-uniform in the angle of incidence, the alignment technique is sensitive to line width.